ABSTRACT
BACE-1 (beta-site amyloid precursor protein cleaving enzyme), a prominent target in Alzheimer's disease drug discovery efforts, was surveyed using Tethering technology to discover small molecule fragment ligands that bind to the enzyme active site. Screens of a library of >15000 thiol-containing fragments versus a panel of BACE-1 active site cysteine mutants under redox-controlled conditions revealed several novel amine-containing fragments that could be selectively captured by subsets of the tethering sites. For one such hit class, defined by a central aminobenzylpiperidine (ABP) moiety, X-ray crystal structures of BACE mutant-disulfide conjugates revealed that the fragment bound by engaging both catalytic aspartates with hydrogen bonds. The affinities of ABP fragments were improved by structure-guided chemistry, first for conjugation as thiol-containing fragments and then for stand-alone, noncovalent inhibition of wild-type (WT) BACE-1 activity. Crystallography confirmed that the inhibitors bound in exactly the same mode as the disulfide-conjugated fragments that were originally selected from the screen. The ABP ligands represent a new type of nonpeptidic BACE-1 inhibitor motif that has not been described in the aspartyl protease literature and may serve as a starting point for the development of BACE-1-directed Alzheimer's disease therapeutics.
Subject(s)
Amyloid Precursor Protein Secretases/antagonists & inhibitors , Drug Discovery/methods , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Amyloid Precursor Protein Secretases/chemistry , Amyloid Precursor Protein Secretases/genetics , Amyloid Precursor Protein Secretases/metabolism , Biocatalysis , Catalytic Domain , Cysteine , Drug Evaluation, Preclinical , Enzyme Inhibitors/metabolism , Humans , Ligands , Models, Molecular , Molecular Conformation , Mutation , Peptides/chemistry , Piperidines/chemistry , Piperidines/metabolism , Structure-Activity RelationshipABSTRACT
The identification of a selective CDK2, 7, 9 inhibitor 4 with improved permeability is described. Compound 4 exhibits comparable CDK selectivity profile to SNS-032, but shows improved permeability and higher bioavailability in mice.
Subject(s)
Oxazoles/chemistry , Oxazoles/pharmacokinetics , Thiazoles/chemistry , Thiazoles/pharmacokinetics , Animals , Biological Availability , Mice , PermeabilityABSTRACT
Modifications of the isonipecotic acid fragment of SNS-032 results in analogs which are more permeable and lower effluxed than SNS-032. The enantiomerically pure synthesis and the in vivo profile of analog 20 is described.
Subject(s)
Cyclin-Dependent Kinase 2/antagonists & inhibitors , Isonipecotic Acids/chemistry , Oxazoles/chemical synthesis , Thiazoles/chemical synthesis , Animals , Combinatorial Chemistry Techniques , Isonipecotic Acids/pharmacology , Mice , Molecular Structure , Oxazoles/chemistry , Oxazoles/pharmacology , Stereoisomerism , Structure-Activity Relationship , Thiazoles/chemistry , Thiazoles/pharmacologyABSTRACT
A series of 2-amino-pyrazolopyridines was designed and synthesized as Polo-like kinase (Plk) inhibitors based on a low micromolar hit. The SAR was developed to provide compounds exhibiting low nanomolar inhibitory activity of Plk1; the phenotype of treated cells is consistent with Plk1 inhibition. A co-crystal structure of one of these compounds with zPlk1 confirms an ATP-competitive binding mode.
Subject(s)
Cell Cycle Proteins/antagonists & inhibitors , Chemistry, Pharmaceutical/methods , Protein Serine-Threonine Kinases/antagonists & inhibitors , Proto-Oncogene Proteins/antagonists & inhibitors , Pyrazoles/chemical synthesis , Pyridines/chemical synthesis , Adenosine Triphosphate/chemistry , Amino Acid Motifs , Cell Cycle , Crystallography, X-Ray , Drug Design , Humans , Inhibitory Concentration 50 , Models, Chemical , Molecular Conformation , Phenotype , Pyrazoles/chemistry , Pyrazoles/pharmacology , Pyridines/chemistry , Pyridines/pharmacology , Structure-Activity Relationship , Polo-Like Kinase 1ABSTRACT
Disulfide Tethering was applied to the active site of human caspase-1, resulting in the discovery of a novel, tricyclic molecular fragment that selectively binds in S4. This fragment was developed into a class of potent inhibitors of human caspase-1. Several key analogues determined the optimal distance of the tricycle from the catalytic residues, the relative importance of various features of the tricycle, and the importance of the linker.
Subject(s)
Caspase Inhibitors , Enzyme Inhibitors/chemical synthesis , Heterocyclic Compounds, 3-Ring/chemistry , Heterocyclic Compounds, 3-Ring/pharmacology , Binding Sites , Caspase 1/chemistry , Catalysis , Enzyme Inhibitors/pharmacology , Humans , Structure-Activity RelationshipABSTRACT
Caspase-1 is a key endopeptidase responsible for the post-translational processing of the IL-1beta and IL-18 cytokines and small-molecule inhibitors that modulate the activity of this enzyme are predicted to be important therapeutic treatments for many inflammatory diseases. A fragment-assembly approach, accompanied by structural analysis, was employed to generate caspase-1 inhibitors. With the aid of Tethering with extenders (small molecules that bind to the active-site cysteine and contain a free thiol), two novel fragments that bound to the active site and made a disulfide bond with the extender were identified by mass spectrometry. Direct linking of each fragment to the extender generated submicromolar reversible inhibitors that significantly reduced secretion of IL-1beta but not IL-6 from human peripheral blood mononuclear cells. Thus, Tethering with extenders facilitated rapid identification and synthesis of caspase-1 inhibitors with cell-based activity and subsequent structural analyses provided insights into the enzyme's ability to accommodate different inhibitor-binding modes in the active site.
Subject(s)
Caspase Inhibitors , Combinatorial Chemistry Techniques/methods , Cysteine Proteinase Inhibitors/chemistry , Binding Sites/drug effects , Caspase 1/chemistry , Crystallography, X-Ray , Cysteine Proteinase Inhibitors/metabolism , Cysteine Proteinase Inhibitors/pharmacology , Drug Design , Humans , Interleukin-1/antagonists & inhibitors , Interleukin-1/blood , Interleukin-6/antagonists & inhibitors , Interleukin-6/blood , Leukocytes, Mononuclear/drug effects , Leukocytes, Mononuclear/enzymology , Leukocytes, Mononuclear/metabolism , Models, Molecular , Protein Binding/drug effects , SolubilityABSTRACT
The design and synthesis of a series of novel, reversible, small molecule inhibitors of caspase-3 are described.
Subject(s)
Caspase Inhibitors , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/pharmacology , Aldehydes/chemistry , Caspase 3 , Indicators and Reagents , Ketones/chemistry , Kinetics , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Conformation , Stereoisomerism , Structure-Activity RelationshipABSTRACT
The design, synthesis, and in vitro activities of a series of potent and selective small-molecule inhibitors of caspase-3 are described. From extended tethering, a salicylic acid fragment was identified as having binding affinity for the S(4) pocket of caspase-3. X-ray crystallography and molecular modeling of the initial tethering hit resulted in the synthesis of 4, which reversibly inhibited caspase-3 with a K(i) = 40 nM. Further optimization led to the identification of a series of potent and selective inhibitors with K(i) values in the 20-50 nM range. One of the most potent compounds in this series, 66b, inhibited caspase-3 with a K(i) = 20 nM and selectivity of 8-500-fold for caspase-3 vs a panel of seven caspases (1, 2, and 4-8). A high-resolution X-ray cocrystal structure of 4 and 66b supports the predicted binding modes of our compounds with caspase-3.
